I was wondering why wasn't there on the server any area/multi-weld tool. Since I use Precision Alignment (and I don't think I'm alone) for my builds 95% of the time, I don't weld my stuff until I'm done with the hull. With adv. dupe 2 this is easily possible, since it has area copy option.
Currently when I'm done, I just go into singleplayer and weld my props to a single prop with smart weld, but I'm sure any other one would work, or even a custom one if necessary.
The only downsides of doing this in singleplayer are the loadtimes, and the fact that I can't weld what isn't there (server specific entities).